Yeah, that's a classic problem of "in development" games. I do say in the "skills help" section to not buy any skill before you need it to help prevent situations like that.
But, perhaps I'll also add another section there showing which skills are currently usable in the most recent version of the game. I wouldn't know how to make that info visible in the main screen when it is already quite crowded.
Another issue that might be important to address somehow is to let the players know (or at least have some hints) which skills they will need with a girl so they can work towards those without needing a walkthrough (which I'm trying to avoid at all costs - the game should provide most of the info/hints you need to get the desirable outcome the player seeks). I'm evaluating some ideas at the moment. The next update might already have a system to help with this problem.
Thanks for the feedback and suggestions.